import requests
import xarray as xr
import ujson
import s3fs
import fsspec
from tqdm import tqdm
from glob import glob
import os
import pathlib
import hvplot.xarray
from kerchunk.hdf import SingleHdf5ToZarr
from kerchunk.combine import MultiZarrToZarr
# The xarray produced from the reference file throws a SerializationWarning for each variable. Will need to explore why
import warnings
warnings.simplefilter("ignore")PO.DAAC ECCO SSH
Reading ECCO Sea Surface Height (SSH) Data Using Kerchunk Reference File
Many of NASA’s current and legacy data collections are archive in netCDF4 format. By itself, netCDF4 are not cloud optimized and reading these files can take as long from a personal/local work environment as it takes to read the data from a working environment deployed in the cloud. Using Kerchunk, we can treat these files as cloud optimized assets by creating metadata json file describing existing netCDF4 files, their chunks, and where to access them. The json reference files can be read in using Zarr and Xarray for efficient reads and fast processing.
Requirements
1. AWS instance running in us-west-2
NASA Earthdata Cloud data in S3 can be directly accessed via temporary credentials; this access is limited to requests made within the US West (Oregon) (code: us-west-2) AWS region.
2. Earthdata Login
An Earthdata Login account is required to access data, as well as discover restricted data, from the NASA Earthdata system. Thus, to access NASA data, you need Earthdata Login. Please visit https://urs.earthdata.nasa.gov to register and manage your Earthdata Login account. This account is free to create and only takes a moment to set up.
3. netrc File
You will need a netrc file containing your NASA Earthdata Login credentials in order to execute the notebooks. A netrc file can be created manually within text editor and saved to your home directory. For additional information see: Authentication for NASA Earthdata.
Import required packages
Create Dask client to process the output json file in parallel
Generating the Kerchunk reference file can take some time depending on the internal structure of the data. Dask allows us to execute the reference file generation process in parallel, thus speeding up the overall process.
import dask
from dask.distributed import Client
client = Client(n_workers=4)
client2022-05-11 15:27:29,674 - distributed.diskutils - INFO - Found stale lock file and directory '/home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/dask-worker-space/worker-mezhdsy7', purging
/srv/conda/envs/notebook/lib/python3.9/contextlib.py:126: UserWarning: Creating scratch directories is taking a surprisingly long time. This is often due to running workers on a network file system. Consider specifying a local-directory to point workers to write scratch data to a local disk.
next(self.gen)
Client
Client-ddf55e52-d13e-11ec-818c-b6609e8b92a4
| Connection method: Cluster object | Cluster type: distributed.LocalCluster |
| Dashboard: http://127.0.0.1:41805/status |
Cluster Info
LocalCluster
a24e60d3
| Dashboard: http://127.0.0.1:41805/status | Workers: 4 |
| Total threads: 4 | Total memory: 15.18 GiB |
| Status: running | Using processes: True |
Scheduler Info
Scheduler
Scheduler-8e045442-a409-4c3b-8c8c-a95470883931
| Comm: tcp://127.0.0.1:36901 | Workers: 4 |
| Dashboard: http://127.0.0.1:41805/status | Total threads: 4 |
| Started: Just now | Total memory: 15.18 GiB |
Workers
Worker: 0
| Comm: tcp://127.0.0.1:34235 | Total threads: 1 |
| Dashboard: http://127.0.0.1:42845/status | Memory: 3.80 GiB |
| Nanny: tcp://127.0.0.1:37927 | |
| Local directory: /home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/dask-worker-space/worker-869qv5xb | |
Worker: 1
| Comm: tcp://127.0.0.1:40997 | Total threads: 1 |
| Dashboard: http://127.0.0.1:41189/status | Memory: 3.80 GiB |
| Nanny: tcp://127.0.0.1:35257 | |
| Local directory: /home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/dask-worker-space/worker-3mo0d80c | |
Worker: 2
| Comm: tcp://127.0.0.1:46429 | Total threads: 1 |
| Dashboard: http://127.0.0.1:42211/status | Memory: 3.80 GiB |
| Nanny: tcp://127.0.0.1:34287 | |
| Local directory: /home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/dask-worker-space/worker-o2fvmao4 | |
Worker: 3
| Comm: tcp://127.0.0.1:41615 | Total threads: 1 |
| Dashboard: http://127.0.0.1:41507/status | Memory: 3.80 GiB |
| Nanny: tcp://127.0.0.1:43053 | |
| Local directory: /home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/dask-worker-space/worker-9u77hywd | |
Get temporary S3 credentials
Temporary S3 credentials need to be passed to AWS. Note, these credentials must be refreshed after 1 hour.
s3_cred_endpoint = {
'podaac':'https://archive.podaac.earthdata.nasa.gov/s3credentials',
'lpdaac':'https://data.lpdaac.earthdatacloud.nasa.gov/s3credentials',
'ornldaac':'https://data.ornldaac.earthdata.nasa.gov/s3credentials',
'gesdisc':'https://data.gesdisc.earthdata.nasa.gov/s3credentials'
}def get_temp_creds():
temp_creds_url = s3_cred_endpoint['podaac']
return requests.get(temp_creds_url).json()temp_creds_req = get_temp_creds()Direct Access a single netCDF4 file
Pass temporary credentials to our filesystem object to access the S3 assets
fs = s3fs.S3FileSystem(
anon=False,
key=temp_creds_req['accessKeyId'],
secret=temp_creds_req['secretAccessKey'],
token=temp_creds_req['sessionToken']
)url = 's3://podaac-ops-cumulus-protected/ECCO_L4_SSH_05DEG_MONTHLY_V4R4/SEA_SURFACE_HEIGHT_mon_mean_2015-01_ECCO_V4r4_latlon_0p50deg.nc's3_file_obj = fs.open(url, mode='rb')Time how long it takes to directly access a cloud asset for comparisons later.
%%time
xr_ds = xr.open_dataset(s3_file_obj, chunks='auto', engine='h5netcdf')
xr_dsCPU times: user 228 ms, sys: 8.51 ms, total: 237 ms
Wall time: 272 ms
<xarray.Dataset>
Dimensions: (time: 1, latitude: 360, longitude: 720, nv: 2)
Coordinates:
* time (time) datetime64[ns] 2015-01-16T12:00:00
* latitude (latitude) float32 -89.75 -89.25 -88.75 ... 89.25 89.75
* longitude (longitude) float32 -179.8 -179.2 -178.8 ... 179.2 179.8
time_bnds (time, nv) datetime64[ns] dask.array<chunksize=(1, 2), meta=np.ndarray>
latitude_bnds (latitude, nv) float32 dask.array<chunksize=(360, 2), meta=np.ndarray>
longitude_bnds (longitude, nv) float32 dask.array<chunksize=(720, 2), meta=np.ndarray>
Dimensions without coordinates: nv
Data variables:
SSH (time, latitude, longitude) float32 dask.array<chunksize=(1, 360, 720), meta=np.ndarray>
SSHIBC (time, latitude, longitude) float32 dask.array<chunksize=(1, 360, 720), meta=np.ndarray>
SSHNOIBC (time, latitude, longitude) float32 dask.array<chunksize=(1, 360, 720), meta=np.ndarray>
Attributes: (12/57)
acknowledgement: This research was carried out by the Jet Pr...
author: Ian Fenty and Ou Wang
cdm_data_type: Grid
comment: Fields provided on a regular lat-lon grid. ...
Conventions: CF-1.8, ACDD-1.3
coordinates_comment: Note: the global 'coordinates' attribute de...
... ...
time_coverage_duration: P1M
time_coverage_end: 2015-02-01T00:00:00
time_coverage_resolution: P1M
time_coverage_start: 2015-01-01T00:00:00
title: ECCO Sea Surface Height - Monthly Mean 0.5 ...
uuid: 088d03b8-4158-11eb-876b-0cc47a3f47f1Specify a list of S3 URLs
Data Collection: ECCO_L4_SSH_05DEG_MONTHLY_V4R4
Time Range: 2015
urls = ['s3://podaac-ops-cumulus-protected/ECCO_L4_SSH_05DEG_MONTHLY_V4R4/SEA_SURFACE_HEIGHT_mon_mean_2014-12_ECCO_V4r4_latlon_0p50deg.nc',
's3://podaac-ops-cumulus-protected/ECCO_L4_SSH_05DEG_MONTHLY_V4R4/SEA_SURFACE_HEIGHT_mon_mean_2015-01_ECCO_V4r4_latlon_0p50deg.nc',
's3://podaac-ops-cumulus-protected/ECCO_L4_SSH_05DEG_MONTHLY_V4R4/SEA_SURFACE_HEIGHT_mon_mean_2015-02_ECCO_V4r4_latlon_0p50deg.nc',
's3://podaac-ops-cumulus-protected/ECCO_L4_SSH_05DEG_MONTHLY_V4R4/SEA_SURFACE_HEIGHT_mon_mean_2015-03_ECCO_V4r4_latlon_0p50deg.nc',
's3://podaac-ops-cumulus-protected/ECCO_L4_SSH_05DEG_MONTHLY_V4R4/SEA_SURFACE_HEIGHT_mon_mean_2015-04_ECCO_V4r4_latlon_0p50deg.nc',
's3://podaac-ops-cumulus-protected/ECCO_L4_SSH_05DEG_MONTHLY_V4R4/SEA_SURFACE_HEIGHT_mon_mean_2015-05_ECCO_V4r4_latlon_0p50deg.nc',
's3://podaac-ops-cumulus-protected/ECCO_L4_SSH_05DEG_MONTHLY_V4R4/SEA_SURFACE_HEIGHT_mon_mean_2015-06_ECCO_V4r4_latlon_0p50deg.nc',
's3://podaac-ops-cumulus-protected/ECCO_L4_SSH_05DEG_MONTHLY_V4R4/SEA_SURFACE_HEIGHT_mon_mean_2015-07_ECCO_V4r4_latlon_0p50deg.nc',
's3://podaac-ops-cumulus-protected/ECCO_L4_SSH_05DEG_MONTHLY_V4R4/SEA_SURFACE_HEIGHT_mon_mean_2015-08_ECCO_V4r4_latlon_0p50deg.nc',
's3://podaac-ops-cumulus-protected/ECCO_L4_SSH_05DEG_MONTHLY_V4R4/SEA_SURFACE_HEIGHT_mon_mean_2015-09_ECCO_V4r4_latlon_0p50deg.nc',
's3://podaac-ops-cumulus-protected/ECCO_L4_SSH_05DEG_MONTHLY_V4R4/SEA_SURFACE_HEIGHT_mon_mean_2015-10_ECCO_V4r4_latlon_0p50deg.nc',
's3://podaac-ops-cumulus-protected/ECCO_L4_SSH_05DEG_MONTHLY_V4R4/SEA_SURFACE_HEIGHT_mon_mean_2015-11_ECCO_V4r4_latlon_0p50deg.nc',
's3://podaac-ops-cumulus-protected/ECCO_L4_SSH_05DEG_MONTHLY_V4R4/SEA_SURFACE_HEIGHT_mon_mean_2015-12_ECCO_V4r4_latlon_0p50deg.nc']Generate the Kerchunk reference files.
Define a function to generate the Kerchunk reference files. These files can take a little time to generate.
def gen_json(u):
so = dict(
mode= "rb",
anon= False,
default_fill_cache= False,
default_cache_type= "none"
)
with fs.open(u, **so) as infile:
h5chunks = SingleHdf5ToZarr(infile, u, inline_threshold=300)
with open(f"jsons/{u.split('/')[-1]}.json", 'wb') as outf:
outf.write(ujson.dumps(h5chunks.translate()).encode())Create output jsons directory if one does not exist.
pathlib.Path('./jsons/').mkdir(exist_ok=True)Use the Dask Delayed function to create the Kerchunk reference file for each URL from the list of URLs in parallel
%%time
reference_files = []
for url in urls:
ref = dask.delayed(gen_json)(url)
reference_files.append(ref)
reference_files_compute = dask.compute(*reference_files)CPU times: user 195 ms, sys: 83.4 ms, total: 278 ms
Wall time: 1.38 s
fs_ref_list = fsspec.filesystem('file')reference_list = sorted([x for x in fs_ref_list.ls('jsons') if '.json' in x])
reference_list['/home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/jsons/SEA_SURFACE_HEIGHT_mon_mean_2014-12_ECCO_V4r4_latlon_0p50deg.nc.json',
'/home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/jsons/SEA_SURFACE_HEIGHT_mon_mean_2015-01_ECCO_V4r4_latlon_0p50deg.nc.json',
'/home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/jsons/SEA_SURFACE_HEIGHT_mon_mean_2015-02_ECCO_V4r4_latlon_0p50deg.nc.json',
'/home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/jsons/SEA_SURFACE_HEIGHT_mon_mean_2015-03_ECCO_V4r4_latlon_0p50deg.nc.json',
'/home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/jsons/SEA_SURFACE_HEIGHT_mon_mean_2015-04_ECCO_V4r4_latlon_0p50deg.nc.json',
'/home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/jsons/SEA_SURFACE_HEIGHT_mon_mean_2015-05_ECCO_V4r4_latlon_0p50deg.nc.json',
'/home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/jsons/SEA_SURFACE_HEIGHT_mon_mean_2015-06_ECCO_V4r4_latlon_0p50deg.nc.json',
'/home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/jsons/SEA_SURFACE_HEIGHT_mon_mean_2015-07_ECCO_V4r4_latlon_0p50deg.nc.json',
'/home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/jsons/SEA_SURFACE_HEIGHT_mon_mean_2015-08_ECCO_V4r4_latlon_0p50deg.nc.json',
'/home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/jsons/SEA_SURFACE_HEIGHT_mon_mean_2015-09_ECCO_V4r4_latlon_0p50deg.nc.json',
'/home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/jsons/SEA_SURFACE_HEIGHT_mon_mean_2015-10_ECCO_V4r4_latlon_0p50deg.nc.json',
'/home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/jsons/SEA_SURFACE_HEIGHT_mon_mean_2015-11_ECCO_V4r4_latlon_0p50deg.nc.json',
'/home/jovyan/earthdata-cloud-cookbook/examples/PODAAC/jsons/SEA_SURFACE_HEIGHT_mon_mean_2015-12_ECCO_V4r4_latlon_0p50deg.nc.json']
Read single netCDF4 using Kerchunk reference file
Open the first reference file to read into an xarray dataset
with open(reference_list[0]) as j:
reference = ujson.load(j)Set configurations options
s_opts = {'skip_instance_cache':True} #json
r_opts = {'anon':False,
'key':temp_creds_req['accessKeyId'],
'secret':temp_creds_req['secretAccessKey'],
'token':temp_creds_req['sessionToken']} #ncfilesfs_single = fsspec.filesystem("reference",
fo=reference,
ref_storage_args=s_opts,
remote_protocol='s3',
remote_options=r_opts)Read in a single reference object. We get a lot of SerializationWarnings which are ignored here using the warning package.
NOTE, the fill value, data range, min value, and max value may not match the source file. Will need to look into this more.
%%time
m = fs_single.get_mapper("")
ds_single = xr.open_dataset(m, engine="zarr", backend_kwargs={'consolidated':False}, chunks={})
ds_singleCPU times: user 56.3 ms, sys: 26 ms, total: 82.2 ms
Wall time: 221 ms
<xarray.Dataset>
Dimensions: (time: 1, latitude: 360, longitude: 720, nv: 2)
Coordinates:
* latitude (latitude) float32 -89.75 -89.25 -88.75 ... 89.25 89.75
latitude_bnds (latitude, nv) float32 dask.array<chunksize=(360, 2), meta=np.ndarray>
* longitude (longitude) float32 -179.8 -179.2 -178.8 ... 179.2 179.8
longitude_bnds (longitude, nv) float32 dask.array<chunksize=(720, 2), meta=np.ndarray>
* time (time) datetime64[ns] 2014-12-16T12:00:00
time_bnds (time, nv) datetime64[ns] dask.array<chunksize=(1, 2), meta=np.ndarray>
Dimensions without coordinates: nv
Data variables:
SSH (time, latitude, longitude) float32 dask.array<chunksize=(1, 360, 720), meta=np.ndarray>
SSHIBC (time, latitude, longitude) float32 dask.array<chunksize=(1, 360, 720), meta=np.ndarray>
SSHNOIBC (time, latitude, longitude) float32 dask.array<chunksize=(1, 360, 720), meta=np.ndarray>
Attributes: (12/57)
Conventions: CF-1.8, ACDD-1.3
acknowledgement: This research was carried out by the Jet Pr...
author: Ian Fenty and Ou Wang
cdm_data_type: Grid
comment: Fields provided on a regular lat-lon grid. ...
coordinates_comment: Note: the global 'coordinates' attribute de...
... ...
time_coverage_duration: P1M
time_coverage_end: 2015-01-01T00:00:00
time_coverage_resolution: P1M
time_coverage_start: 2014-12-01T00:00:00
title: ECCO Sea Surface Height - Monthly Mean 0.5 ...
uuid: 08a2fc68-4158-11eb-b498-0cc47a3f6943Read multiple netCDF4 files using Kerchunk reference file
Combine the individual reference files into a single time series reference object
%%time
ds_k =[]
for ref in reference_list:
s_opts = s_opts
r_opts = r_opts
fs = fsspec.filesystem("reference",
fo=ref,
ref_storage_args=s_opts,
remote_protocol='s3',
remote_options=r_opts)
m = fs.get_mapper("")
ds_k.append(xr.open_dataset(m, engine="zarr", backend_kwargs={'consolidated':False}, chunks={}))
ds_multi = xr.concat(ds_k, dim='time')
ds_multiCPU times: user 735 ms, sys: 31.4 ms, total: 766 ms
Wall time: 3.57 s
<xarray.Dataset>
Dimensions: (time: 13, latitude: 360, longitude: 720, nv: 2)
Coordinates:
* latitude (latitude) float32 -89.75 -89.25 -88.75 ... 89.25 89.75
latitude_bnds (latitude, nv) float32 -90.0 -89.5 -89.5 ... 89.5 89.5 90.0
* longitude (longitude) float32 -179.8 -179.2 -178.8 ... 179.2 179.8
longitude_bnds (longitude, nv) float32 -180.0 -179.5 -179.5 ... 179.5 180.0
* time (time) datetime64[ns] 2014-12-16T12:00:00 ... 2015-12-16T...
time_bnds (time, nv) datetime64[ns] dask.array<chunksize=(1, 2), meta=np.ndarray>
Dimensions without coordinates: nv
Data variables:
SSH (time, latitude, longitude) float32 dask.array<chunksize=(1, 360, 720), meta=np.ndarray>
SSHIBC (time, latitude, longitude) float32 dask.array<chunksize=(1, 360, 720), meta=np.ndarray>
SSHNOIBC (time, latitude, longitude) float32 dask.array<chunksize=(1, 360, 720), meta=np.ndarray>
Attributes: (12/57)
Conventions: CF-1.8, ACDD-1.3
acknowledgement: This research was carried out by the Jet Pr...
author: Ian Fenty and Ou Wang
cdm_data_type: Grid
comment: Fields provided on a regular lat-lon grid. ...
coordinates_comment: Note: the global 'coordinates' attribute de...
... ...
time_coverage_duration: P1M
time_coverage_end: 2015-01-01T00:00:00
time_coverage_resolution: P1M
time_coverage_start: 2014-12-01T00:00:00
title: ECCO Sea Surface Height - Monthly Mean 0.5 ...
uuid: 08a2fc68-4158-11eb-b498-0cc47a3f6943ds_multi['SSH']<xarray.DataArray 'SSH' (time: 13, latitude: 360, longitude: 720)>
dask.array<concatenate, shape=(13, 360, 720), dtype=float32, chunksize=(1, 360, 720), chunktype=numpy.ndarray>
Coordinates:
* latitude (latitude) float32 -89.75 -89.25 -88.75 ... 88.75 89.25 89.75
* longitude (longitude) float32 -179.8 -179.2 -178.8 ... 178.8 179.2 179.8
* time (time) datetime64[ns] 2014-12-16T12:00:00 ... 2015-12-16T12:00:00
Attributes:
comment: Dynamic sea surface height anomaly above the geoi...
coverage_content_type: modelResult
long_name: Dynamic sea surface height anomaly
standard_name: sea_surface_height_above_geoid
units: m
valid_max: 1.4207719564437866
valid_min: -1.8805772066116333# Commenting for quarto site render
# ds_multi['SSH'].hvplot.image()References
- https://github.com/fsspec/kerchunk
- https://medium.com/pangeo/fake-it-until-you-make-it-reading-goes-netcdf4-data-on-aws-s3-as-zarr-for-rapid-data-access-61e33f8fe685
- https://medium.com/pangeo/cloud-performant-reading-of-netcdf4-hdf5-data-using-the-zarr-library-1a95c5c92314